Isolation and chemical composition of the cytoplasmic membrane of a gram-negative bacterium

Reconciling in vivo and in silico key biological parameters of Pseudomonas putida KT2440 during growth on glucose under carbon-limited condition

Background

Genome scale metabolic reconstructions are developed to efficiently engineer biocatalysts and bioprocesses based on a rational approach. However, in most reconstructions, due to the lack of appropriate measurements, experimentally determined growth parameters are simply taken from literature including other organisms, which reduces the usefulness and suitability of these models. Pseudomonas putida KT2440 is an outstanding biocatalyst given its versatile metabolism, its ability to generate sufficient energy and turnover of NADH and NAD. To apply this strain optimally in industrial production, a previously developed genome-scale metabolic model (iJP815) was experimentally assessed and streamlined to enable accurate predictions of the outcome of metabolic engineering approaches.

Results

To substantially improve the accuracy of the genome scale model (iJP815), continuous bioreactor cultures on a mineral medium with glucose as a sole carbon source were carried out at different dilution rates, which covered pulling analysis of the macromolecular composition of the biomass. Besides, the maximum biomass yield (on substrate) of 0.397 g_DCW · g_glc^-1, the maintenance coefficient of 0.037 g_glc · g_DCW^-1 · h^-1 and the maximum specific growth rate of 0.59 h^-1 were determined. Only the DNA fraction increased with the specific growth rate. This resulted in reliable estimation for the Growth-Associated Maintenance (GAM) of 85 mmol_ATP · g_DCW^-1 and the Non Growth-Associated Maintenance (NGAM) of 3.96 mmol_ATP · g_DCW^-1 · h^-1. Both values were found significantly different from previous assignment as a consequence of a lower yield and higher maintenance coefficient than originally assumed. Contrasting already published ¹³C flux measurements and the improved model allowed for constraining the solution space, by eliminating futile cycles. Furthermore, the model predictions were compared with transcriptomic data at overall good consistency, which helped to identify missing links.

Conclusions

By careful interpretation of growth stoichiometry and kinetics when grown in the presence of glucose, this work reports on an accurate genome scale metabolic model of Pseudomonas putida, providing a solid basis for its use in designing superior strains for biocatalysis. By consideration of substrate specific variation in stoichiometry and kinetics, it can be extended to other substrates and new mutants.

[Preliminary study of the chemical composition of crude membranes of Scopulariopsis brevicaulis (Bainier)]

Whole membrane constituents isolated from Scopulariopsis brevicaulis in culture in vitro have been studied with respect to ultracytological and biochemical composition. The ratio of proteins to lipids is near 1. Neutral lipids and phospholipids have been studied separately. The neutral lipids are triglycerids, diglycerids, free sterols and sterol esters, phospholipids are phosphatidylethanolamine and phosphatidylcholine.

Distribution of lipopolysaccharide and the detection of a new subfraction in the cell envelope of a marine pseudomonad

The three outer layers of the cell envelope of marine pseudomonad B-16, the loosely bound outer layer, the outer membrane, and the periplasmic space layer, are the only ones containing appreciable amounts of both lipid and carbohydrate. These layers and a fraction released into the medium during growth of the cells were examined for the presence of common antigens by double immunodiffusion using anti-whole serum. Each of the layers, the medium fraction, and lipopolysaccharide (LPS) isolated from the organism were shown to contain two or more diffusible components showing reactions of identity. Thus LPS is found in each of the three outer layers of the cell envelope of this gram-negative bacterium. The periplasmic space layer was found to contain a fraction accounting for 20% of the dry weight of the layer, which was sedimentable at 30,000 x g and contained lipid, protein, and carbohydrate. Double-immunodiffusion tests indicated that the fraction contained at least one of the two antigens present in isolated LPS. A particulate material was released by the cells during growth which gave a positive test for 2-keto-3-deoxyoctulosonic acid and cross-reacted serologically with LPS.

Interaction of Mg-2+ with peptidoglycan and its relation to the prevention of lysis of a marine pseudomonad

Intact cells of marine pseudomonad B-16 (ATCC 19855) which have been washed with a solution of NaCl require only 0.001 M MgSO4 and 100 to 300 times this concentration of NaCl or KCl to prevent lysis. Conversion of intact cells to mureinoplasts, a process involving removal of the outer double-track layer (outer membrane) and the periplasmic space layer of the cell wall, approximately doubled the requirement for the three salts to prevent lysis. The formation of protoplasts from mureinoplasts by removing the peptidoglycan layer again doubled the requirement for Na+ and K+ salts but increased the requirement for the Mg-2+ salt 200- to 300-fold. Cells of the marine pseudomonad suspended in solutions containing Mg-2+ salts failed to lyse on subsequent repeated suspension in distilled water, whereas cells presuspended in NaCl lysed immediately. Isolated envelope layers including the peptidoglycan layer, when dialyzed against solutiions containing Mg-2+ salts, retained Mg-2+ after subsequent suspension in distilled water. Envelope layers exposed to solutions of Na+ or K+ salts failed to retain these ions after exposure to distilled water. Na+ displaced Mg-2+ from the cell envelope layers. The results obtained indicate that the capacity of Mg-2+ salts at very low concentration to prevent lysis of intact cells and mureinoplasts of this organism is due primarily to the interaction of Mg-2+ with the peptidoglycan layer of the cell wall. Ion interaction with the layers lying outside of the peptidoglycan layer contributes only a small amount to the mechanical strength of the wall.

Capacity of the outer membrane of a gram-negative marine bacterium in the presence of cations to prevent lysis by Triton X-100

Cells of marine pseudomonad B-16 (ATCC 19855) washed with a solution containing 0.3 M NaCl, 50 mM MgCl2, and 10 mM KCl (complete salts) could be protected from lysis in a hypotonic environment if the suspending medium contained either 20 mM Mg2+, 40 mM Na+, or 300 mM K+. When the outer double-track layer (the outer membrane) of the cell envelope was removed to yield mureinoplasts, the Mg2+, Na+ or K+, requirements to prevent lysis were raised to 80, 210, and 400 mM, respectively. In the presence of 0.1% Triton X-100, 220, 320, and 360 mM Mg2+, Na+ or K+, respectively, prevented lysis of the normal cells. Mureinoplasts and protoplasts, however, lysed instantly in the presence of the detergent at all concentrations of Mg2+, Na+, or K+ tested up to 1.2 M. Thus, the structure of the outer membrane appears to be maintained by appropriate concentrations of Mg2+ or Na+ in a form preventing the penetration of Triton X-100 and thereby protecting the cytoplasmic membrane from dissolution by the detergent. K+ was effective in this capacity with cells washed with complete salts solution but not with cells washed with a solution of NaCl, suggesting that bound Mg2+ was required in the cell wall membrane for K+ to be effective in preventing lysis by the detergent. At high concentrations (1 M) K+ and Mg2+, but not Na+, appeared to destabilize the structure of the outer membrane in the presence of Triton X-100.

Nature of the specificity of alcohol coupling to L-alanine transport into isolated membrane vesicles of a marine pseudomonad

Ethanol stimulated the uptake of l-alanine into isolated membrane vesicles of a marine pseudomonad at a rate and to an extent comparable with that obtained with reduced nicotinamide adenine dinucleotide (NADH) or the artificial electron donor ascorbate-N, N, N', N'-tetramethyl-p-phenylenediamine (ascorbate-TMPD). Methanol and branched-chain alcohols had little or no capacity to energize transport. No quantitative relationship was found between the ability of a compound to induce oxygen uptake and to energize transport, since with ethanol initial rates of oxygen uptake were approximately 4% of that obtained with NADH or ascorbate-TMPD. Cytochrome analysis revealed that NADH and ethanol reduced cytochromes b and c, whereas ascorbate-TMPD coupled primarily at the level of cytochrome c. Approximately 25% of the cytochromes reduced by dithionite were reducible by ethanol. Ethanol reduction of both cytochromes b and c was prevented by 2-heptyl-4-hydroxyquinoline-N-oxide, p-chloromercuribenzoate, N-ethylmaleimide, and iodoacetate. The ethanol- and NADH-energized transport systems for l-alanine were subject to quantitatively similar inhibition by cyanide, 2-heptyl-4-hydroxyquinoline-N-oxide, 2, 4-dinitrophenol, and the sulfhydryl reagents p-chloromercuribenzoate, N-ethylmaleimide, and iodoacetate. In contrast, for ascorbate-TMPD-driven transport, only cyanide and 2, 4-dinitrophenol remained fully effective as inhibitors, p-chloromercuribenzoate was only half as effective, and the other compounds stimulated transport. Inhibition of ethanol oxidation strikingly paralleled the inhibition of ethanol-driven transport for each of the inhibitors, including 2, 4-dinitrophenol. Marked differences between inhibition of oxygen uptake and inhibition of transport were observed when NADH or ascorbate-TMPD were the electron donors. The data indicate that only a small proportion of the respiratory chain complexes in the membrane vesicles are involved in transport and these are efficiently coupled to ethanol oxidation. The results also suggest that when 2, 4-dinitrophenol inhibits transport it is not acting as an uncoupling agent.

Structure and function of the cell envelope of gram-negative bacteria

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Freeze-etching and x-ray diffraction of the isolated double-track layer from the cell wall of a gram-negative marine pseudomonad

The isolated double-track layer of the cell wall of the gram-negative marine pseudomonad studied here contains a cleavage plane. This finding localizes the single cleavage plane of the cell wall and shows that the molecular architecture of this layer provides the lipid-enriched layer which cleaves preferentially in the frozen cell. The observation that the isolated double-track layer of the cell wall is sufficiently ordered at the molecular level to yield a well-defined X-ray diffraction pattern with a d-spacing of 0.44 nm shows that its molecular architecture is very similar to that of true membranes. This specific d-spacing is produced by the highly ordered packing of the hydrophobic portions of phospholipid molecules. Therefore, the double-track layer of the cell wall has been shown, by these two biophysical means, to have a molecular architecture which would allow it to function as the membrane-like "molecular sieve" layer, whose presence has been deduced from physiological data. This layer is important in the retention of cell wall-associated enzymes and in the control of the movement of large molecules through the cell wall.

Specific removal of proteins from the envelope of Escherichia coli by protease treatments

When the envelope fraction of Escherichia coli was treated by trypsin, about 40% of total envelope proteins were removed from the fraction without changing its phospholipid content. Analysis of envelope proteins by acrylamide gel electrophoresis in 0.5% sodium dodecyl sulfate revealed that trypsin treatment was very specific; one of the major proteins (molecular weight, 38,000) and all proteins of molecular weight greater than 70,000 were completely removed by the treatment. On the other hand, three other major proteins were found to be resistant to the treatment, including protein Y, which was previously shown to be related to deoxyribonucleic acid replication. The trypsin treatment of the envelope fractions composed of a five electron-dense layered structure formed vesicles with a triple-layered membrane (two electron-dense layers). Pronase treatment of the envelope fraction removed about 60% of the envelope proteins without changing its phospholipid content. A major protein of molecular weight of 58,000 was found to be the only protein resistant to the Pronase treatment. Application of these treatments is useful for purification and structural studies of envelope proteins.

Characterization of spheroplast membranes of Neisseria meningitidis group B

Spheroplast membranes (spheroplast envelopes) of strain 2091 of group B Neisseria meningitidis were prepared by a procedure that included lysozyme treatment of the cells and osmotic lysis of the resulting spheroplasts. Electron microscopy revealed that the membranes consisted of two unit layers, generally parallel to each other. The membrane preparation migrated as a single component in a 40 to 70% sucrose gradient and consisted of 62% protein, 28% lipid, 9% ribonucleic acid, small amounts of carbohydrate, hexosamine, and deoxyribonucleic acid. When 1 or 10 mug (dry weight) was injected intravenously into rabbits, a mild pyrogenic reaction was elicited. In immunodiffusion tests, immune rabbit serum prepared against spheroplast membranes produced three major precipitin lines, with the homologous antigen solubilized with sodium dodecyl sulfate, and a single line with untreated antigen. The immune serum also reacted with a cell wall antigen, and to a lesser extent with some of the cytoplasmic antigens. Succinate dehydrogenase and reduced nicotinamide adenine dinucleotide (NADH) oxidase activities were found to be associated with the spheroplast membranes. NADH dehydrogenase also was associated with the membranes but was gradually released and recovered in other fractions. Glutamate-oxaloacetate transaminase, glutamate, glucose-6-phosphate, and isocitrate dehydrogenase activities were not found in the membrane preparation. About one-third of these enzymatic activities were recovered in the supernatant fluid after the sedimentation of the spheroplasts and two-thirds were recovered in the cytoplasmic fraction. N-acetylneuraminic acid (NAN)-condensing enzyme and cytidine monophosphate-NAN synthesizing enzyme also were identified in this organism. These enzymes were not associated with the membranes and were recovered from extracts from whole cells, spheroplasts, or cells exposed to osmotic shock, as well as from spheroplast supernatant and shock fluids. It is concluded that the spheroplast membranes of the strain of meningococci used in these studies are typical of those recovered from gram-negative bacteria.